Prepare for release v2.3.6 (#465)

* Prepare for release v2.3.6

* Update gcc version for mac_gcc test to be consistent with current brew bottle

* brew install gcc@12

Author: lcoombe

ChangeLog

@@ -1,3 +1,14 @@
+2023-05-02 Lauren Coombe <lcoombe@bcgsc.ca>
+
+  * Release version 2.3.6
+
+    General:
+    * btllib is now a dependency
+	* Documentation updates
+
+	abyss-rresolver-short:
+	* btllib source code removed due to btllib now being a dependency
+
 2022-05-11 Vladimir Nikolic <vnikolic@bcgsc.ca>
 
   * Release version 2.3.5

Misc/samtobreak.hs

@@ -279,7 +279,7 @@ parseArgs = do
   where
   help = putStr (usageInfo usage options) >> exitSuccess
   tryHelp = "Try 'abyss-samtobreak --help' for more information."
-  version = "abyss-samtobreak (ABySS) 2.3.5\n"
+  version = "abyss-samtobreak (ABySS) 2.3.6\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

azure-pipelines.yml

@@ -6,7 +6,7 @@ jobs:
   - script: |
       rm -f /usr/local/bin/2to3 # brew is having issues with installing Python
       brew update
-      brew install automake boost openmpi google-sparsehash make pandoc ghc 
+      brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@12
     displayName: Install common
   - script: |
       wget https://github.com/bcgsc/btllib/releases/download/v1.5.1/btllib-1.5.1.tar.gz
@@ -15,7 +15,6 @@ jobs:
       tar xzf btllib-1.5.1.tar.gz
       cd btllib-1.5.1
       ./compile
-      pwd
     displayName: Install btllib
   - script: |
       ./autogen.sh

bin/abyss-pe

@@ -414,7 +414,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.3.5"
+	@echo "abyss-pe (ABySS) 2.3.6"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.3.5, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.3.6, abyss-users@bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.5" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.6" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.5" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.6" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.5" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.6" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br